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MIRit

This is the development version of MIRit; to use it, please install the devel version of Bioconductor.

Integrate microRNA and gene expression to decipher pathway complexity


Bioconductor version: Development (3.19)

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

Author: Jacopo Ronchi [aut, cre] , Maria Foti [fnd]

Maintainer: Jacopo Ronchi <jacopo.ronchi at unimib.it>

Citation (from within R, enter citation("MIRit")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MIRit")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MIRit")
Integrate miRNA and gene expression data with MIRit HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Network, NetworkEnrichment, NetworkInference, Pathways, Software, SystemsBiology
Version 0.99.13
In Bioconductor since BioC 3.19 (R-4.4)
License GPL (>= 3)
Depends MultiAssayExperiment, R (>= 4.4.0)
Imports AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, readxl, Rgraphviz(>= 2.44.0), rlang, stats, utils
System Requirements
URL https://github.com/jacopo-ronchi/MIRit
Bug Reports https://github.com/jacopo-ronchi/MIRit/issues
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Suggests BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0)
Linking To Rcpp
Enhances
Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MIRit_0.99.13.tar.gz
Windows Binary
macOS Binary (x86_64) MIRit_0.99.13.tgz
macOS Binary (arm64) MIRit_0.99.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIRit
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MIRit
Bioc Package Browser https://code.bioconductor.org/browse/MIRit/
Package Short Url https://bioconductor.org/packages/MIRit/
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